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        Package&nbsp;weblogolib
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<!-- ==================== PACKAGE DESCRIPTION ==================== -->
<h1 class="epydoc">Package weblogolib</h1><p class="nomargin-top"><span class="codelink"><a href="weblogolib-pysrc.html">source&nbsp;code</a></span></p>
<pre class="literalblock">

WebLogo (http://code.google.com/p/weblogo/) is a tool for creating sequence 
logos from biological sequence alignments.  It can be run on the command line,
as a standalone webserver, as a CGI webapp, or as a python library.

The main WebLogo webserver is located at http://weblogo.threeplusone.com

Please consult the manual for installation instructions and more information:
(Also located in the weblogolib/htdocs subdirectory.)

    http://weblogo.threeplusone.com/manual.html

For help on the command line interface run
    ./weblogo --help

To build a simple logo run
    ./weblogo  &lt; cap.fa &gt; logo0.eps
    
To run as a standalone webserver at localhost:8080 
    ./weblogo --serve

To create a logo in python code:
    &gt;&gt;&gt; from weblogolib import *
    &gt;&gt;&gt; fin = open('cap.fa')
    &gt;&gt;&gt; seqs = read_seq_data(fin) 
    &gt;&gt;&gt; data = LogoData.from_seqs(seqs)
    &gt;&gt;&gt; options = LogoOptions()
    &gt;&gt;&gt; options.title = &quot;A Logo Title&quot;
    &gt;&gt;&gt; format = LogoFormat(data, options)
    &gt;&gt;&gt; fout = open('cap.eps', 'w') 
    &gt;&gt;&gt; eps_formatter( data, format, fout)


-- Distribution and Modification --
This package is distributed under the new BSD Open Source License. 
Please see the LICENSE.txt file for details on copyright and licensing.
The WebLogo source code can be downloaded from 
http://code.google.com/p/weblogo/

WebLogo requires Python 2.5, 2.6 or 2.7, and the python
array package 'numpy' (http://www.scipy.org/Download)

Generating logos in PDF or bitmap graphics formats require that the ghostscript
program 'gs' be installed. Scalable Vector Graphics (SVG) format also requires 
the program 'pdf2svg'.

</pre>

<hr />
<div class="fields">      <p><strong>Version:</strong>
        3.2
      </p>
</div><!-- ==================== SUBMODULES ==================== -->
<a name="section-Submodules"></a>
<table class="summary" border="1" cellpadding="3"
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  <td align="left" colspan="2" class="table-header">
    <span class="table-header">Submodules</span></td>
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  <tr><td class="summary">
  <ul class="nomargin">
    <li class="private"> <strong class="uidlink"><a href="weblogolib._cgi-module.html">weblogolib._cgi</a></strong>    </li>
    <li class="private"> <strong class="uidlink"><a href="weblogolib._cli-module.html">weblogolib._cli</a></strong>    </li>
    <li> <strong class="uidlink"><a href="weblogolib.color-module.html">weblogolib.color</a></strong>: <em class="summary">Color specifications using CSS2 (Cascading Style Sheet) syntax.</em>    </li>
    <li> <strong class="uidlink"><a href="weblogolib.colorscheme-module.html">weblogolib.colorscheme</a></strong>: <em class="summary">Popular color codings for nucleic and amino acids.</em>    </li>
    <li> <strong class="uidlink"><a href="weblogolib.logomath-module.html">weblogolib.logomath</a></strong>    </li>
  </ul></td></tr>
</table>

<br />
<!-- ==================== CLASSES ==================== -->
<a name="section-Classes"></a>
<table class="summary" border="1" cellpadding="3"
       cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
  <td align="left" colspan="2" class="table-header">
    <span class="table-header">Classes</span></td>
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    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
        <a href="weblogolib.GhostscriptAPI-class.html" class="summary-name">GhostscriptAPI</a><br />
      Interface to the command line program Ghostscript ('gs')
    </td>
  </tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
        <a href="weblogolib.LogoOptions-class.html" class="summary-name">LogoOptions</a><br />
      A container for all logo formatting options.
    </td>
  </tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
        <a href="weblogolib.LogoFormat-class.html" class="summary-name">LogoFormat</a><br />
      Specifies the format of the logo.
    </td>
  </tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
        <a href="weblogolib.LogoData-class.html" class="summary-name">LogoData</a><br />
      The data needed to generate a sequence logo.
    </td>
  </tr>
</table>
<!-- ==================== FUNCTIONS ==================== -->
<a name="section-Functions"></a>
<table class="summary" border="1" cellpadding="3"
       cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
  <td align="left" colspan="2" class="table-header">
    <span class="table-header">Functions</span></td>
</tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
      <table width="100%" cellpadding="0" cellspacing="0" border="0">
        <tr>
          <td><span class="summary-sig"><a name="pdf_formatter"></a><span class="summary-sig-name">pdf_formatter</span>(<span class="summary-sig-arg">data</span>,
        <span class="summary-sig-arg">format</span>,
        <span class="summary-sig-arg">fout</span>)</span><br />
      Generate a logo in PDF format.</td>
          <td align="right" valign="top">
            <span class="codelink"><a href="weblogolib-pysrc.html#pdf_formatter">source&nbsp;code</a></span>
            
          </td>
        </tr>
      </table>
      
    </td>
  </tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
      <table width="100%" cellpadding="0" cellspacing="0" border="0">
        <tr>
          <td><span class="summary-sig"><a name="jpeg_formatter"></a><span class="summary-sig-name">jpeg_formatter</span>(<span class="summary-sig-arg">data</span>,
        <span class="summary-sig-arg">format</span>,
        <span class="summary-sig-arg">fout</span>)</span><br />
      Generate a logo in JPEG format.</td>
          <td align="right" valign="top">
            <span class="codelink"><a href="weblogolib-pysrc.html#jpeg_formatter">source&nbsp;code</a></span>
            
          </td>
        </tr>
      </table>
      
    </td>
  </tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
      <table width="100%" cellpadding="0" cellspacing="0" border="0">
        <tr>
          <td><span class="summary-sig"><a name="png_formatter"></a><span class="summary-sig-name">png_formatter</span>(<span class="summary-sig-arg">data</span>,
        <span class="summary-sig-arg">format</span>,
        <span class="summary-sig-arg">fout</span>)</span><br />
      Generate a logo in PNG format.</td>
          <td align="right" valign="top">
            <span class="codelink"><a href="weblogolib-pysrc.html#png_formatter">source&nbsp;code</a></span>
            
          </td>
        </tr>
      </table>
      
    </td>
  </tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
      <table width="100%" cellpadding="0" cellspacing="0" border="0">
        <tr>
          <td><span class="summary-sig"><a name="png_print_formatter"></a><span class="summary-sig-name">png_print_formatter</span>(<span class="summary-sig-arg">data</span>,
        <span class="summary-sig-arg">format</span>,
        <span class="summary-sig-arg">fout</span>)</span><br />
      Generate a logo in PNG format with print quality (600 DPI) resolution.</td>
          <td align="right" valign="top">
            <span class="codelink"><a href="weblogolib-pysrc.html#png_print_formatter">source&nbsp;code</a></span>
            
          </td>
        </tr>
      </table>
      
    </td>
  </tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
      <table width="100%" cellpadding="0" cellspacing="0" border="0">
        <tr>
          <td><span class="summary-sig"><a name="txt_formatter"></a><span class="summary-sig-name">txt_formatter</span>(<span class="summary-sig-arg">logodata</span>,
        <span class="summary-sig-arg">format</span>,
        <span class="summary-sig-arg">fout</span>)</span><br />
      Create a text representation of the logo data.</td>
          <td align="right" valign="top">
            <span class="codelink"><a href="weblogolib-pysrc.html#txt_formatter">source&nbsp;code</a></span>
            
          </td>
        </tr>
      </table>
      
    </td>
  </tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
      <table width="100%" cellpadding="0" cellspacing="0" border="0">
        <tr>
          <td><span class="summary-sig"><a name="eps_formatter"></a><span class="summary-sig-name">eps_formatter</span>(<span class="summary-sig-arg">logodata</span>,
        <span class="summary-sig-arg">format</span>,
        <span class="summary-sig-arg">fout</span>)</span><br />
      Generate a logo in Encapsulated Postscript (EPS)</td>
          <td align="right" valign="top">
            <span class="codelink"><a href="weblogolib-pysrc.html#eps_formatter">source&nbsp;code</a></span>
            
          </td>
        </tr>
      </table>
      
    </td>
  </tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
      <table width="100%" cellpadding="0" cellspacing="0" border="0">
        <tr>
          <td><span class="summary-sig"><a name="default_formatter"></a><span class="summary-sig-name">default_formatter</span>(<span class="summary-sig-arg">logodata</span>,
        <span class="summary-sig-arg">format</span>,
        <span class="summary-sig-arg">fout</span>)</span><br />
      Generate a logo in Encapsulated Postscript (EPS)</td>
          <td align="right" valign="top">
            <span class="codelink"><a href="weblogolib-pysrc.html#eps_formatter">source&nbsp;code</a></span>
            
          </td>
        </tr>
      </table>
      
    </td>
  </tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
      <table width="100%" cellpadding="0" cellspacing="0" border="0">
        <tr>
          <td><span class="summary-sig"><a name="base_distribution"></a><span class="summary-sig-name">base_distribution</span>(<span class="summary-sig-arg">percentCG</span>)</span></td>
          <td align="right" valign="top">
            <span class="codelink"><a href="weblogolib-pysrc.html#base_distribution">source&nbsp;code</a></span>
            
          </td>
        </tr>
      </table>
      
    </td>
  </tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
      <table width="100%" cellpadding="0" cellspacing="0" border="0">
        <tr>
          <td><span class="summary-sig"><a name="equiprobable_distribution"></a><span class="summary-sig-name">equiprobable_distribution</span>(<span class="summary-sig-arg">length</span>)</span></td>
          <td align="right" valign="top">
            <span class="codelink"><a href="weblogolib-pysrc.html#equiprobable_distribution">source&nbsp;code</a></span>
            
          </td>
        </tr>
      </table>
      
    </td>
  </tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
      <table width="100%" cellpadding="0" cellspacing="0" border="0">
        <tr>
          <td><span class="summary-sig"><a href="weblogolib-module.html#read_seq_data" class="summary-sig-name">read_seq_data</a>(<span class="summary-sig-arg">fin</span>,
        <span class="summary-sig-arg">input_parser</span>=<span class="summary-sig-default">seq_io.read</span>,
        <span class="summary-sig-arg">alphabet</span>=<span class="summary-sig-default">None</span>,
        <span class="summary-sig-arg">ignore_lower_case</span>=<span class="summary-sig-default">False</span>,
        <span class="summary-sig-arg">max_file_size</span>=<span class="summary-sig-default">0</span>)</span><br />
      Read sequence data from the input stream and return a seqs object.</td>
          <td align="right" valign="top">
            <span class="codelink"><a href="weblogolib-pysrc.html#read_seq_data">source&nbsp;code</a></span>
            
          </td>
        </tr>
      </table>
      
    </td>
  </tr>
</table>
<!-- ==================== VARIABLES ==================== -->
<a name="section-Variables"></a>
<table class="summary" border="1" cellpadding="3"
       cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
  <td align="left" colspan="2" class="table-header">
    <span class="table-header">Variables</span></td>
</tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
        <a href="weblogolib-module.html#description" class="summary-name">description</a> = <code title="&quot;Create sequence logos from biological sequence alignments.&quot;">&quot;Create sequence logos from biological sequence <code class="variable-ellipsis">...</code></code>
    </td>
  </tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
        <a href="weblogolib-module.html#classic" class="summary-name">classic</a> = <code title="ColorScheme([ColorGroup(&quot;G&quot;, &quot;orange&quot;), ColorGroup(&quot;TU&quot;, &quot;red&quot;), Color\
Group(&quot;C&quot;, &quot;blue&quot;), ColorGroup(&quot;A&quot;, &quot;green&quot;)])">ColorScheme([ColorGroup(&quot;G&quot;, &quot;orange&quot;), ColorGroup(&quot;<code class="variable-ellipsis">...</code></code>
    </td>
  </tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
        <a href="weblogolib-module.html#std_color_schemes" class="summary-name">std_color_schemes</a> = <code title="{&quot;auto&quot;: None, &quot;monochrome&quot;: monochrome, &quot;base pairing&quot;: base_pairing,\
 &quot;classic&quot;: classic, &quot;hydrophobicity&quot;: hydrophobicity, &quot;chemistry&quot;: ch\
emistry, &quot;charge&quot;: charge,}">{&quot;auto&quot;: None, &quot;monochrome&quot;: monochrome, &quot;<code class="variable-ellipsis">...</code></code>
    </td>
  </tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
        <a href="weblogolib-module.html#default_color_schemes" class="summary-name">default_color_schemes</a> = <code title="{unambiguous_protein_alphabet: hydrophobicity, unambiguous_rna_alphabe\
t: base_pairing, unambiguous_dna_alphabet: base_pairing}">{unambiguous_protein_alphabet: hydroph<code class="variable-ellipsis">...</code></code>
    </td>
  </tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
        <a href="weblogolib-module.html#std_units" class="summary-name">std_units</a> = <code title="{&quot;bits&quot;: 1./ log(2), &quot;nats&quot;: 1., &quot;digits&quot;: 1./ log(10), &quot;kT&quot;: 1., &quot;kJ/\
mol&quot;: 8.314472* 298.15/ 1000., &quot;kcal/mol&quot;: 1.987* 298.15/ 1000., &quot;prob\
ability&quot;: None,}">{&quot;bits&quot;: 1./ log(2), &quot;nats&quot;: 1., &quot;digits&quot;: 1./ log<code class="variable-ellipsis">...</code></code>
    </td>
  </tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
        <a name="std_sizes"></a><span class="summary-name">std_sizes</span> = <code title="{&quot;small&quot;: 5.4, &quot;medium&quot;: 5.4* 2, &quot;large&quot;: 5.4* 3}">{&quot;small&quot;: 5.4, &quot;medium&quot;: 5.4* 2, &quot;large&quot;: 5.4* 3}</code>
    </td>
  </tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
        <a href="weblogolib-module.html#std_alphabets" class="summary-name">std_alphabets</a> = <code title="{'protein': unambiguous_protein_alphabet, 'rna': unambiguous_rna_alpha\
bet, 'dna': unambiguous_dna_alphabet}">{'protein': unambiguous_protein_alphabet, 'rna<code class="variable-ellipsis">...</code></code>
    </td>
  </tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
        <a href="weblogolib-module.html#std_percentCG" class="summary-name">std_percentCG</a> = <code title="{'H. sapiens': 40., 'E. coli': 50.5, 'S. cerevisiae': 38., 'C. elegans\
': 36., 'D. melanogaster': 43., 'M. musculus': 42., 'T. thermophilus':\
 69.4,}">{'H. sapiens': 40., 'E. coli': 50.5, 'S. cerev<code class="variable-ellipsis">...</code></code>
    </td>
  </tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
        <a href="weblogolib-module.html#formatters" class="summary-name">formatters</a> = <code title="{'eps': eps_formatter, 'pdf': pdf_formatter, 'png': png_formatter, 'pn\
g_print': png_print_formatter, 'jpeg': jpeg_formatter, 'svg': svg_form\
atter, 'logodata': txt_formatter,}">{'eps': eps_formatter, 'pdf': pdf_formatter, 'png<code class="variable-ellipsis">...</code></code>
    </td>
  </tr>
</table>
<!-- ==================== FUNCTION DETAILS ==================== -->
<a name="section-FunctionDetails"></a>
<table class="details" border="1" cellpadding="3"
       cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
  <td align="left" colspan="2" class="table-header">
    <span class="table-header">Function Details</span></td>
</tr>
</table>
<a name="read_seq_data"></a>
<div>
<table class="details" border="1" cellpadding="3"
       cellspacing="0" width="100%" bgcolor="white">
<tr><td>
  <table width="100%" cellpadding="0" cellspacing="0" border="0">
  <tr valign="top"><td>
  <h3 class="epydoc"><span class="sig"><span class="sig-name">read_seq_data</span>(<span class="sig-arg">fin</span>,
        <span class="sig-arg">input_parser</span>=<span class="sig-default">seq_io.read</span>,
        <span class="sig-arg">alphabet</span>=<span class="sig-default">None</span>,
        <span class="sig-arg">ignore_lower_case</span>=<span class="sig-default">False</span>,
        <span class="sig-arg">max_file_size</span>=<span class="sig-default">0</span>)</span>
  </h3>
  </td><td align="right" valign="top"
    ><span class="codelink"><a href="weblogolib-pysrc.html#read_seq_data">source&nbsp;code</a></span>&nbsp;
    </td>
  </tr></table>
  
  <pre class="literalblock">
Read sequence data from the input stream and return a seqs object. 

The environment variable WEBLOGO_MAX_FILE_SIZE overides the max_file_size argument.
Used to limit the load on the WebLogo webserver.

</pre>
  <dl class="fields">
  </dl>
</td></tr></table>
</div>
<br />
<!-- ==================== VARIABLES DETAILS ==================== -->
<a name="section-VariablesDetails"></a>
<table class="details" border="1" cellpadding="3"
       cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
  <td align="left" colspan="2" class="table-header">
    <span class="table-header">Variables Details</span></td>
</tr>
</table>
<a name="description"></a>
<div>
<table class="details" border="1" cellpadding="3"
       cellspacing="0" width="100%" bgcolor="white">
<tr><td>
  <h3 class="epydoc">description</h3>
  
  <dl class="fields">
  </dl>
  <dl class="fields">
    <dt>Value:</dt>
      <dd><table><tr><td><pre class="variable">
&quot;Create sequence logos from biological sequence alignments.&quot;
</pre></td></tr></table>
</dd>
  </dl>
</td></tr></table>
</div>
<a name="classic"></a>
<div>
<table class="details" border="1" cellpadding="3"
       cellspacing="0" width="100%" bgcolor="white">
<tr><td>
  <h3 class="epydoc">classic</h3>
  
  <dl class="fields">
  </dl>
  <dl class="fields">
    <dt>Value:</dt>
      <dd><table><tr><td><pre class="variable">
ColorScheme([ColorGroup(&quot;G&quot;, &quot;orange&quot;), ColorGroup(&quot;TU&quot;, &quot;red&quot;), Color<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
Group(&quot;C&quot;, &quot;blue&quot;), ColorGroup(&quot;A&quot;, &quot;green&quot;)])
</pre></td></tr></table>
</dd>
  </dl>
</td></tr></table>
</div>
<a name="std_color_schemes"></a>
<div>
<table class="details" border="1" cellpadding="3"
       cellspacing="0" width="100%" bgcolor="white">
<tr><td>
  <h3 class="epydoc">std_color_schemes</h3>
  
  <dl class="fields">
  </dl>
  <dl class="fields">
    <dt>Value:</dt>
      <dd><table><tr><td><pre class="variable">
{&quot;auto&quot;: None, &quot;monochrome&quot;: monochrome, &quot;base pairing&quot;: base_pairing,<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
 &quot;classic&quot;: classic, &quot;hydrophobicity&quot;: hydrophobicity, &quot;chemistry&quot;: ch<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
emistry, &quot;charge&quot;: charge,}
</pre></td></tr></table>
</dd>
  </dl>
</td></tr></table>
</div>
<a name="default_color_schemes"></a>
<div>
<table class="details" border="1" cellpadding="3"
       cellspacing="0" width="100%" bgcolor="white">
<tr><td>
  <h3 class="epydoc">default_color_schemes</h3>
  
  <dl class="fields">
  </dl>
  <dl class="fields">
    <dt>Value:</dt>
      <dd><table><tr><td><pre class="variable">
{unambiguous_protein_alphabet: hydrophobicity, unambiguous_rna_alphabe<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
t: base_pairing, unambiguous_dna_alphabet: base_pairing}
</pre></td></tr></table>
</dd>
  </dl>
</td></tr></table>
</div>
<a name="std_units"></a>
<div>
<table class="details" border="1" cellpadding="3"
       cellspacing="0" width="100%" bgcolor="white">
<tr><td>
  <h3 class="epydoc">std_units</h3>
  
  <dl class="fields">
  </dl>
  <dl class="fields">
    <dt>Value:</dt>
      <dd><table><tr><td><pre class="variable">
{&quot;bits&quot;: 1./ log(2), &quot;nats&quot;: 1., &quot;digits&quot;: 1./ log(10), &quot;kT&quot;: 1., &quot;kJ/<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
mol&quot;: 8.314472* 298.15/ 1000., &quot;kcal/mol&quot;: 1.987* 298.15/ 1000., &quot;prob<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
ability&quot;: None,}
</pre></td></tr></table>
</dd>
  </dl>
</td></tr></table>
</div>
<a name="std_alphabets"></a>
<div>
<table class="details" border="1" cellpadding="3"
       cellspacing="0" width="100%" bgcolor="white">
<tr><td>
  <h3 class="epydoc">std_alphabets</h3>
  
  <dl class="fields">
  </dl>
  <dl class="fields">
    <dt>Value:</dt>
      <dd><table><tr><td><pre class="variable">
{'protein': unambiguous_protein_alphabet, 'rna': unambiguous_rna_alpha<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
bet, 'dna': unambiguous_dna_alphabet}
</pre></td></tr></table>
</dd>
  </dl>
</td></tr></table>
</div>
<a name="std_percentCG"></a>
<div>
<table class="details" border="1" cellpadding="3"
       cellspacing="0" width="100%" bgcolor="white">
<tr><td>
  <h3 class="epydoc">std_percentCG</h3>
  
  <dl class="fields">
  </dl>
  <dl class="fields">
    <dt>Value:</dt>
      <dd><table><tr><td><pre class="variable">
{'H. sapiens': 40., 'E. coli': 50.5, 'S. cerevisiae': 38., 'C. elegans<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
': 36., 'D. melanogaster': 43., 'M. musculus': 42., 'T. thermophilus':<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
 69.4,}
</pre></td></tr></table>
</dd>
  </dl>
</td></tr></table>
</div>
<a name="formatters"></a>
<div>
<table class="details" border="1" cellpadding="3"
       cellspacing="0" width="100%" bgcolor="white">
<tr><td>
  <h3 class="epydoc">formatters</h3>
  
  <dl class="fields">
  </dl>
  <dl class="fields">
    <dt>Value:</dt>
      <dd><table><tr><td><pre class="variable">
{'eps': eps_formatter, 'pdf': pdf_formatter, 'png': png_formatter, 'pn<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
g_print': png_print_formatter, 'jpeg': jpeg_formatter, 'svg': svg_form<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
atter, 'logodata': txt_formatter,}
</pre></td></tr></table>
</dd>
  </dl>
</td></tr></table>
</div>
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